# PolypSense3D Dataset

## Overview

PolypSense3D is the first comprehensive dataset spanning virtual simulations, physical models, and clinical scenarios for polyp analysis. This dataset systematically collects and annotates over 10,000 frames containing:

- RGB images
- Dense depth data
- Accurate millimeter-scale polyp measurements

PolypSense3D addresses critical gaps in existing datasets by providing comprehensive data for lesion quantification tasks and supporting various computer vision applications in medical imaging.

## Dataset Components

PolypSense3D consists of three distinct datasets:

1. **Virtual Dataset**: Simulated polyp scenarios with perfect ground truth annotations
2. **Physical Model Dataset**: Real-world phantom models with controlled conditions
3. **Clinical Dataset**: Actual clinical cases with expert annotations

## Applications

This dataset supports research and development in:
- Depth estimation
- Polyp segmentation
- 3D reconstruction
- Lesion quantification
- Medical image analysis

## File Structure

Clinical Dataset
   ├─── Clinical Dataset For PolypSense3D.md # This documentation file
   ├─── calibrations # Calibration and lens tracking data
   │  ├─── XX(Random Number)_XX(Lens ID)/ # Calibration images for a specific lens
   │  │  └─── *.png # Checkerboard calibration images
   │  ├─── camera.xlsx # Camera intrinsic and distortion parameters
   │  └─── video_info.xlsx # Table mapping videos to Lens IDs
   ├─── labeled_data # Labeled data
   │  ├─── depth # Coarse depth annotations
   │  │  ├─── json/ # Biopsy forceps point annotations (JSON format)
   │  │  ├─── rgb/ # Clear video frames of biopsy forceps closing action (JPG format)
   │  │  └─── depth_gt.xlsx # Depth ground truth 
   │  ├─── segmentation # Precise polyp segmentation masks
   │  │  ├─── mask/ # Manual polyp segmentation masks (PNG format)
   │  │  └─── rgb/ # Corresponding clear polyp video frames (JPG format)
   │  ├─── size # Polyp size annotations
   │  │  ├─── json/ # Biopsy forceps open for comparison point annotations (JSON format)
   │  │  ├─── rgb/ # Clear video frames of biopsy forceps open for polyp comparison (JPG format)
   │  │  └─── size_gt.xlsx # Size ground truth
   ├─── polyp_frame # Polyp video frame image data
   │  └─── sequenceXXX/
   │    └─── polypY/
   │      └─── frame_XXXX.jpg
   └─── polyp_video # Polyp video data
     └─── sequenceXXX/
       └─── polypY/
         └─── polypY.mp4

Physical Dataset
    ├─── Physical Dataset For PolypSense3D.md # This documentation file
    ├─── camera.xlsx # Camera parameters (Excel file)
    ├─── polys_size.xlsx # Polygon size measurements
    ├─── images/ # Extracted video frames (PNG)
    │  └───  *.png # Extracted video frame with polyp
    ├─── masks/ # Corresponding segmentation masks (PNG)
    │  └───  *.png # segmentation mask with polyp
    ├─── videos/ # Source video files (WMV)
    │  └───  *.wmv # video files with polyp
    └───  calibration/ # Camera calibration data (PNG)
        ├── 12_9_3/ # Calibration set 1
        │  └───  *.png # the calibration board with 12 × 9 × 3 mm.
        ├── 4_5_3/ # Calibration set 2
        │  └───  *.png # the calibration board with 4 × 5 × 3 mm.
        └── FOV/ # Field of view calibration
           └─── *.png # the photo for field of view calibration
           
Virtual Dataset For PolypSense3D
    ├─── Virtual Dataset For PolypSense3D.md # This documentation file
    ├─── depth_estimation/ # Depth estimation data
    │  ├─── camera.txt # Camera parameters file
    │  ├─── depths/ # Depth maps directory （PNG）
    │  │  └─── *.png # Depth maps（PNG）
    │  ├───  images/ # Original images directory （JPG）
    │  │  └─── *.jpg # Original image
    │  ├───  position_rotation.csv # Camera position and rotation parameters
    ├─── image_segmentation/  # Image segmentation data
    │  ├─── images/ # Original images directory （PNG）
    │  │  └─── *.png # Original image
    │  ├─── masks/ # Segmentation masks directory （PNG）
    │  │  └─── *.png # Corresponding Segmentation Masks
    └─── polyp_estimation/ # Polyp estimation data
        ├─── polys_size.xlsx # Polyp size data sheet
        ├─── depths/ # Depth maps directory （PNG）
        │  └─── *.png # Corresponding Depth maps
        ├───images/ # Images directory （PNG）
        │  └─── *.png # Original image
        └────masks/ # Masks directory （PNG）
            └─── *.png # Corresponding Segmentation Masks

## Citation

If you use this dataset in your research, please cite our work (citation information to be provided in the full documentation).